[BioC] Unable to load xps

[cstrato]

Dear Jorge,

Could you please answer the following questions and/or try the following:

- I assume that you have installed XQuartz?

- Are you running R from xterm or from Terminal.app?
(Using R.app will probably not work.)

- Is the absolute path to libGui.so:
/Users/jorgemelendez/my_rnaseq_exp/root/libGui.so

- I see that you did export ROOTSYS etc in .bash_profile. I do not know 
if this may be the reason but I am always putting this in .bashrc in my 
home directory.

- Probably for Mountain Lion the following line is no longer necessary:
export DYLD_LIBRARY_PATH=$ROOTSYS/lib:$DYLD_LIBRARY_PATH

- You probably refer to this thread:
https://www.stat.math.ethz.ch/pipermail/bioconductor/2013-July/053690.html
In this case the user told me that downloading the compiled version from:
ftp://root.cern.ch/root/root_v5.34.05.macosx64-10.8-i386.tar.gz
did finally solve his problem.

- Maybe you could try to compile root from source, i.e. unpack root in 
e.g. your home directory and then do:
$ cd root
$ ./configure macosx64
$ make
$ . bin/thisroot.sh

- How did you install xps? Maybe it will help to compile xps, e.g.:
R CMD INSTALL xps_1.20.3.tar.gz

Best regards,
Christian


On 9/10/13 5:36 PM, Jorge Melendez wrote:
> Hello Christian
> Thanks for the quick response!
> Yes, I am using root_v5.34.05.macosx64-10.8-i386.tar
> Best
> Jorge
>
> On Tue, Sep 10, 2013 at 10:29 AM, cstrato <cstrato at aon.at> wrote:
>> Dear Jorge,
>>
>> Which file did you download from the ROOT website?
>>
>> Please note that the README file says:
>>     For Mountain Lion there exists a 64 bit binary:
>>     root_v5.34.05.macosx64-10.8-i386.tar.gz
>>
>> Best regards,
>> Christian
>> _._._._._._._._._._._._._._._._._._
>> C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
>> V.i.e.n.n.a           A.u.s.t.r.i.a
>> e.m.a.i.l:        cstrato at aon.at
>> _._._._._._._._._._._._._._._._._._
>>
>>
>>
>>
>> On 9/10/13 5:04 PM, Jorge Melendez [guest] wrote:
>>>
>>> Hi!
>>> As someone else on the list, I am having trouble loading xps in a mac. I
>>> am using OSX 10.8, R 3.0.1.  I used the latest precompiled binary and
>>> installed root at ~/my_rnaseq_exp/root. I changed my .bash_profile with
>>> export ROOTSYS=/Users/jorgemelendez/my_rnaseq_exp/root
>>> export PATH=$ROOTSYS/bin:$PATH
>>> export LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH
>>> export DYLD_LIBRARY_PATH=$ROOTSYS/lib:$DYLD_LIBRARY_PATH
>>> Root root runs fine, but when trying to load xps in R:
>>>
>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>>     unable to load shared object
>>> '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/xps/libs/xps.so':
>>>
>>> dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/xps/libs/xps.so,
>>> 6): Library not loaded: @rpath/libGui.so
>>>     Referenced from:
>>> /Library/Frameworks/R.framework/Versions/3.0/Resources/library/xps/libs/xps.so
>>>     Reason: image not found
>>> Error: package or namespace load failed for ‘xps’
>>>
>>>
>>> Can you help?
>>> Thanks a lot
>>>
>>>    -- output of sessionInfo():
>>>
>>> R version 3.0.1 (2013-05-16)
>>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>>
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> loaded via a namespace (and not attached):
>>> [1] tools_3.0.1
>>>
>>> --
>>> Sent via the guest posting facility at bioconductor.org.
>>>
>>
>
>
>